Borneo contains some of the oldest rainforest in the world and is characterised by exceptionally high biodiversity being the centre of evolution and radiation of many species of plants and animals endemic to the region. Endemism in freshwater organisms has been particularly demonstrated for fishes, amphibians and some aquatic invertebrates (especially insects), but the diversity of aquatic taxa is poorly understood relative to that of the terrestrial flora and fauna. An even more incomplete understanding characterises what is known of the diversity of parasitic groups in this region and most particularly of those groups that are poorly known overall. The aim of the NHM Sabah Expedition Freshwater Team was to undertake a combination of environmental and targeted sampling to explore the diversity of parasitic groups across a range of sites and habitats. A key component of our work involved adopting environmental sampling to significantly improve on discovery rates of novel endoparasitic lineages and thereby avoid the necessity of finding parasites within host organisms. A second objective was to gain better understanding of the diversity of freshwater bryozoans (Phylum Bryozoa, Class Phylactolaemata) and their myxozoan parasites. We will provide a summary of our activities and results thereby demonstrating how our programme of work is revealing novel biodiversity of aquatic life.